Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Computes the loglikelihood of the DAISIE model with cladespecific
diversitydependence given colonization and branching times for lineages on
an island, and a set of model parameters. The output is a loglikelihood value
 (pars1, pars2, datalist, methode = "lsodes",
CS_version = 1, abstolint = 1e16, reltolint = 1e10)

pars1 
Contains the model parameters: pars1[1]
corresponds to lambda^c (cladogenesis rate) pars1[2] corresponds
to mu (extinction rate) pars1[3] corresponds to K (cladelevel
carrying capacity) pars1[4] corresponds to gamma (immigration
rate) pars1[5] corresponds to lambda^a (anagenesis rate)
pars1[6] corresponds to lambda^c (cladogenesis rate) for an optional
subset of the species pars1[7] corresponds to mu (extinction
rate) for an optional subset of the species pars1[8] corresponds
to K (cladelevel carrying capacity) for an optional subset of the
species pars1[9] corresponds to gamma (immigration rate) for an
optional subset of the species pars1[10] corresponds to lambda^a
(anagenesis rate) for an optional subset of the species pars1[11]
corresponds to p_f (fraction of mainland species that belongs to the second
subset of species The elements 6:10 and 11 are optional, that is,pars1
should either contain 5, 10 or 11 elements. If 10, then the fraction of
potential colonists of type 2 is computed from the data. If 11, then
pars1[11] is used, overruling any information in the data.

pars2 
Contains the model settings pars2[1] corresponds
to lx = length of ODE variable x pars2[2] corresponds to ddmodel
= diversitydependent model, model of diversitydependence, which can be one
of ddmodel = 0 : no diversity dependence ddmodel = 1 : linear
dependence in speciation rate ddmodel = 11: linear dependence in
speciation rate and in immigration rate ddmodel = 2 : exponential
dependence in speciation rate ddmodel = 21: exponential dependence in
speciation rate and in immigration rate pars2[3] corresponds
to cond = setting of conditioning cond = 0 : conditioning on island
age cond = 1 : conditioning on island age and nonextinction of the
island biota pars2[4] sets whether parameters and likelihood
should be printed (1) or not (0)

datalist 
Data object containing information on colonisation and
branching times. This object can be generated using the DAISIE_dataprep
function, which converts a userspecified data table into a data object, but
the object can of course also be entered directly. It is an R list object
with the following elements. The first element of the list has two or
three components: $island_age  the island age Then,
depending on whether a distinction between types is made, we have:
$not_present  the number of mainland lineages that are not present
on the island or: $not_present_type1  the number of mainland
lineages of type 1 that are not present on the island
$not_present_type2  the number of mainland lineages of type 2 that
are not present on the island The remaining elements of the list
each contains information on a single colonist lineage on the island and has
5 components: $colonist_name  the name of the species or
clade that colonized the island $branching_times  island age and
stem age of the population/species in the case of Nonendemic,
Nonendemic_MaxAge and Endemic anagenetic species. For cladogenetic species
these should be island age and branching times of the radiation including
the stem age of the radiation. $stac  the status of the colonist
* Non_endemic_MaxAge: 1 * Endemic: 2 * Endemic&Non_Endemic:
3 * Non_Endemic: 4 * Endemic_Singleton_MaxAge: 5 *
Endemic_Clade_MaxAge: 6 * Endemic&Non_Endemic_Clade_MaxAge: 7
$missing_species  number of island species that were not sampled for
particular clade (only applicable for endemic clades) $type1or2 
whether the colonist belongs to type 1 or type 2

methode 
Method of the ODEsolver. See package deSolve for details.
Default is "lsodes"

CS_version 
For internal testing purposes only. Default is 1, the
original DAISIE code.

abstolint 
Absolute tolerance of the integration

reltolint 
Relative tolerance of the integration

The loglikelihood
Rampal S. Etienne & Bart Haegeman
Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
Equilibrium and nonequilibrium dynamics simultaneously operate in the
Galapagos islands. Ecology Letters 18: 844852.
DAISIE_ML
, DAISIE_sim
 ::()
pars1 = (0.195442017,0.087959583,,0.002247364,0.873605049,
3755.202241,8.909285094,14.99999923,0.002247364,0.873605049,0.163)
pars2 = (100,11,0,1)
(pars1,pars2,)

xieshu95/TestTrasie documentation built on Dec. 18, 2019, 7:34 a.m.